A World of Hurt: Isolation
by Alipeeps
Summary: Part of a series of Shep whumpy tag fics to Season 3 eps. The Real World tag. SPOILERS FOR THE REAL WORLD! He wasn't there when she woke up. NOW COMPLETE.
1. Chapter 1

_This is the tag fic for The Real World.__ There was no real way to get physical whump into this episode so I've gone with good old-fashioned emotional angst instead! Hope you enjoy..._

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He wasn't there when she woke up.

Carson's staff, their faces stern behind the hazmat masks, had pulled him bodily from Elizabeth's isolation tent and marched him straight into an isolation area of his very own. This one had walls instead of plastic sheets, a solid door instead of a simple zipper and clear windows to allow observation. The first thing his escorts did was take away his gun and as he saw the fear and distrust in his eyes it hit him hard, like a punch to the gut; the risk he had taken. It was worth it though, he told himself as they left the room, the door sliding shut behind them with the distinctive sound of the lock engaging. It had to be. She would make it. She would. The alternative was… No, he couldn't… he wouldn't think about that. They'd lost enough… _he'd_ lost enough and every death was a burden, a weight on his soul.

He'd lost men under his command, civilians he was supposed to protect, even his own CO, but if he lost Elizabeth… if he lost any of them, of his family… The fact that he felt even the slightest bit thankful that the people they had lost, the people he had failed to protect, had not been those he had cared most about, was yet another burden for him to carry, another millstone of self-recrimination. His team… Elizabeth, Carson… they were all he had.

He'd opened his soul, as best as he was able, to Teyla on the Daedalus, sharing with her the bare, painful truth, and it had been no maudlin dramatics, no heroic gesture, when he'd said he would die for any of them. He would. And even that was a reason for guilt; an ugly little voice telling him that that was the coward's way out, that he was simply running from his responsibilities… that dying was easy, easier than living with the pain of loss.

He paced the small room restlessly, his body stiff with tension, his mind racing, wondering what was happening just down the hall… he spun on his heel as the door hummed open to admit more hazmat-suited medics, rolling an ancient scanner into the room with them.

"How is she?" he demanded. "Has there been any change?"

Their expressions were guarded, non-committal, their voices muffled by the suits as they side-stepped his questions with vague platitudes and reassurance.

"You'll need to lie down, sir."

John felt frustration pulling his shoulder muscles into knots. He knew this was necessary. He'd put himself in this situation, done it willingly in the faint hope of getting through to Elizabeth, giving her that small connection that could help her to hold on, to fight. But that knowledge didn't make this any easier, didn't quell the nerves in his stomach, the tiny, spiteful thread of fear that lurked at the back of his mind, telling him that it was too late, that they were going to lose her and there was nothing he could do about it. Being cut off like this, not knowing what was happening, was torture and his movements were jerky with impatience as he reluctantly hoisted himself onto the exam bed and laid back stiffly.

As tense as he was, the combination of bulky-suited medics bustling around the bed, their faces all but obscured in their protective hoods, and the heavy arm of the scanner looming over him as it was swung into place over the bed felt threateningly claustrophobic and it was all he could do to hold himself still and not jump from the bed and make a run for it. He fisted his hands into the starched white sheets beneath him and gritted his teeth as the scanner powered up with a low hum and began its steady hover up the length of his body.

As he lay there, biting down on the fear and worry, watching the sleek white surface of the scanner slowly block out his view of the ceiling above, he couldn't help but think back to the last time he had lain fully-clothed on a medical bed, the gentle hum of the scanner vibrating overhead. He'd kept his eyes closed that time, focusing his attention inwards, hyper aware of his body and the way it was starting to feel… different. He frowned. Much as Elizabeth had doubted his assertation at the time, he _had_ been able to feel something happening to him, feel the virus slowly changing him. He wondered if it had been the same for Elizabeth, if she had been able to feel – was still able to feel – what the nanites were doing to her. And what if the nanites were now in him, too? Would he feel it? Would he…?

He closed his eyes and forced himself to try and relax, pushing out a long, slow breath and focusing his attention inwards. He concentrated, feeling the rise and fall of his chest with each breath in and out, the weight of his limbs pressing into the mattress of the bed as he tried to relax his muscles. He felt tense, his body thrumming with nervous energy… but otherwise normal. There was no sense of wrongness, no indefinable awareness of gradual physiological changes that would eventually wreak havoc on his body, his mind… He opened his eyes abruptly, a sigh of frustration escaping him. If the nanites were inside him now, then he had no awareness of it.

Maybe Elizabeth hadn't either… she'd seemed perfectly fine. Hours had passed since Niam's attack and she'd shown no symptoms, no hint of suspicion that anything was wrong… right up until she'd simply collapsed in the control room, a dead weight in his arms as he radioed frantically for help. He couldn't help but dwell on that terrible moment, on the terrifying suddenness of her collapse, the feel of her body utterly limp in his grip. For a moment he hadn't even been sure that she'd been breathing and cold fear had gripped his heart. He'd laid her gently on the ground, instinctively applying the field triage training that had been drilled into him as he checked her airways, breathing and pulse. He'd been operating on autopilot, his subconscious mind pushing him into action even as his higher brain function struggled with shock and fear.

He'd had the luxury of indulging that shock for about ten minutes… the amount of time it had taken for Carson to get to the control room, load Elizabeth onto a gurney, get her back to the infirmary and run his first scan. From that moment on, the city had been on high alert and John was officially in command of the Atlantis Expedition. The appearance of the nanites on that first scan had thrown the infirmary into chaos, off-duty medical staff who they could be reasonably certain had been nowhere near Elizabeth being called in to gear up in hazmat suits while Carson himself had rapidly enacted isolation protocols and herded everyone who'd been near Elizabeth, including John, into a secure section of the infirmary.

They'd scanned everyone, starting with Carson who hurried off immediately to suit up and return to his patient. The scans had been clear, even John's who'd held her in his arms, who'd touched the bare skin of her arms, her neck, her face as he'd laid her on the floor of the control room and checked to be sure she was still alive. He didn't know why the nanites hadn't spread then and he didn't know whether they had spread this time. Could he have dodged the bullet twice? Or was what had happened to Elizabeth happening to him now? Were the tiny, aggressive robots multiplying and proliferating in his body, waiting until they were large enough in number to attack his brain, to drop him where he stood and leave him helpless as they slowly took over his body?

The scanner ground to a halt with a decisive clunk and he sat up abruptly, turning his attention to the hazmat suit holding the datapad.

"Well? What's the verdict?" His voice came out rough, tinged with impatience.

The medic – the bluish lights lining the faceplate tended to wash out and distort color but he caught a glimpse of what looked like a stray curl of red hair and realised belatedly that it was Dr Nielsen under the helmet – looked up from the scan results and gave a cautious nod. "It looks clear, Colonel," she told him.

The surge of relief he felt was immediately drowned out by the need to get out of here, to get back in there and find out what was happening. Surely they'd have told him if something had… if…? He made to slide from the bed and found a thick-gloved hand on his shoulder, stopping the movement.

"I'm sorry, Colonel Sheppard. You can't leave yet."

He stared up at the burly medic – Steiger, wasn't that his name? – and felt frustration simmering towards anger. "Why not?" he ground out. "The scan is clear…"

"We don't know how long it may take for an infection to show up on the scans," Neilsen interrupted and he heard genuine regret in her muffled voice. "There was no sign of any nanites when we scanned Dr Weir's neck following the replicator's initial attack on her," she explained. "It could take hours for a small number of nanites to reproduce enough to become visible to the scanner."

"_Hours_?" John's stomach lurched.

Steiger's hand was still firm on his shoulder. "Sorry, sir," he rumbled. "You're to remain in isolation. Dr Beckett's orders."

He felt his shoulders sag with defeat, the stress and tension of the past few hours suddenly catching up to him and draining the strength from his body. The momentary reprieve had been just that; momentary, fleeting. He could still be infected. He was still a security risk. And he was still locked up, cut off from his team, from Elizabeth who at this very minute could be… He pushed that thought away wearily. Whatever was happening just down the hall, there was nothing more he could do to help. He didn't protest when Neilsen mentioned blood tests, obediently rolling up his sleeve for the needle. He sat on the exam bed, his thoughts distant, only vaguely aware of the continued bustle of the hazmat-suited medics.

He was brought out of his brooding by a sudden banging sound; a fist on glass. He looked up, surprised to see a broadly grinning McKay pounding on the observation window. McKay's voice was muffled by the thick glass but nonetheless John's heart skipped a beat as he read the words on Rodney's lips.

"She woke up!"

McKay's smile was glorious, heartfelt, and he felt an answering grin stretch his face as a little bit of weight lifted from his shoulders. For a moment he felt light, almost floating. She did it. She'd fought back. She'd won. For today at least, he wasn't going to lose anyone.

He hadn't been there to see it, hadn't been there when she woke up, but that was okay. And he might still be infected, might yet find himself unconscious in a plastic tent with tiny robots attacking his brain, but that was okay too. Because she'd survived, she was going to live… and that made it all worthwhile.

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_TBC..._


	2. Chapter 2

She was on her feet again, seemingly fully recovered, before they let him out of isolation.

He only found out afterwards what had happened as he'd cooled his heels for hours, through multiple scans and blood tests; how she'd woken just briefly at first, her body exhausted from the fight; how Carson had kept her for observation after she'd woken properly; her description of the fantasy world the nanites had created in their attempt to subjugate her will, her consciousness.

The whole thing, from Elizabeth's collapse to her eventual awakening, had taken only five hours. They kept him in quarantine for eight, just to be on the safe side, re-scanning him every hour. It had been a long, slow, restless wait with only hazmat-suited medics for company. His team had been busy, their concern naturally focused on Elizabeth. Once she was discharged from the infirmary he'd had a few brief visits; Rodney had waved a datapad vaguely and rattled off a stream of incomprehensible technobabble before dashing off, his attention clearly already focused on interpreting the data they had collected from the nanite attack; Teyla had attempted to make small talk through the glass windows, her smile of relief belying her mild scolding about the risks he had taken; Ronon had simply nodded, his silent regard conveying an understanding and acceptance of John's actions.

Carson, on the other hand, had suited up and come into the isolation room to check for himself the scan results and to chastise John in person for his "irresponsible" behaviour. John had schooled his face into a neutral expression, neither too remorseful (because he didn't regret his actions for a second) nor too stubborn (if Carson thought John wasn't taking the lecture on board it would just go on for longer) and nodded at appropriate intervals, whilst inside he just felt like grinning. It had worked; that was all that mattered.

Eventually Carson had left, the fatigue evident in his posture, the warmth of relief in his eyes, saying without words that, risky and foolish or not, Carson was as glad as John of the successful outcome of his actions. The only person who hadn't come by was Elizabeth and Carson had explained that he'd sent her to her quarters to get some rest; her body had recovered quickly from the nanite infestation but the experience had left her understandably shaken. John didn't know then what she had seen, what she had experienced during her coma, only that his theory had been right; the nanites had been messing with her mind, trapping her in an imagined scenario designed to undermine her body's natural defences, to subliminally persuade her not to fight them.

The thought of what she might have experienced, might have lived through, in those short (endless) five hours had sent a chill of apprehension through him. As time had passed he had allowed himself a cautious hope that his continued lack of symptoms was a good sign, indicating that the nanites had not spread to him, but the medics had remained sternly non-committal, refusing to release him and continuing their periodic scan and checks. The lurking fear that he would share Elizabeth's fate had still lingered in the back of his mind, his imagination throwing out scenarios of what might happen to him, what insidious fantasies the nanites might create to entrap him. Would knowing what had happened to Elizabeth help him, he'd wondered? Would he retain that memory, that knowledge, if they invaded his brain? Would he know that something was wrong, that what he saw wasn't real? Or would he be as lost as Elizabeth, living an imagined life while his body lay still and dying in a plastic tent?

He'd pushed those thoughts aside and slipped from his perch on the exam bed, a feeling of barely contained restlessness thrumming through him. Bored and restless from his enforced confinement, he'd paced the room for a while, his thoughts brooding, trying to work off his excess energy. The room was too small though, barely 15 paces in each direction, not enough space to hit any kind of stride, to even stretch his muscles, and with an exam bed, a bulky scanner and anywhere up to five hazmat-suited medics sharing the confined space it wasn't long before his restless wandering was earning him irritated looks from behind tinted faceplates. He'd given up and settled back on the exam bed again when Dr Nielsen informed him in a rather snappish tone that it was time his next blood test – a full 10 minutes before it was due.

As she'd placed another full sample tube to one side and carefully withdrawn the needle, he'd seen her stern expression soften in sympathy. "Not much longer, Colonel," she'd tried to reassure him. He'd nodded, offering her a half-hearted grin. It wasn't her fault he was stuck in here. He had only himself to blame for that… didn't make it any less frustrating though.

He'd moped for a while, perched on the exam bed, his legs swinging absently as he dwelled fruitlessly on what-ifs and might-have-beens. Eventually, annoyed at himself, he'd stretched out on the firm mattress and tried to pass the time by catching a much-needed nap. He'd been awake since the early hours, his nightmares pulling him from a restless sleep, and it was now getting into early evening Atlantis time. The intervening hours had been filled with stress and worry and he'd felt suddenly exhausted, his body crashing as the adrenalin of urgency deserted him. He'd been too wired to rest though, his body still tense from the long hours of growing desperation, his mind unable to switch off from the worry, the excitement, the fear. He'd tossed and turned restlessly, never achieving more than a restless half-doze, plagued by half-formed dreams and fragments of memory.

He'd woken up sweating, a cry dying on his lips, his skin itching with the imagined sensation of millions of tiny robots scurrying around his body, swimming in his blood, harvesting his cells to replicate themselves and swarm and spread and…

He'd sat up abruptly, ignoring the hesitant, uncomfortable concern of the ever-present medics as he swung his legs over the edge of the exam bed and rested his elbows on his knees, letting his head hang down loosely as he focused on calming his thundering pulse, his breathing still a little rapid and shaky. He'd felt a shudder ripple through him and had straightened up, unconsciously rubbing his arms. He'd been in isolation for hours, with hours more to go until he could be given the all clear and for the first time it had hit him what it really meant, the risk he'd taken. Not the risk to himself but the risk to Atlantis; to the expedition, to the lives of his friends. If his desperate move hadn't worked then Elizabeth would probably have died – or worse, been wholly consumed and taken over by nanites, becoming a human form replicator… one who wore a friend's face. And worse than that… he could have been infected too – could still be infected, he'd reminded himself – and could have shared the same fate… leaving the Atlantis team dealing with two devastating personal losses and a possible threat to the city with no-one there to lead them.

He'd felt the sweat turn cold on his skin and in that moment he'd really understood, as no-one else could, the burden of command and the furious chewing out his CO in Afghanistan had given him after he'd risked everything in an effort to save one man…He had put personal feelings over the safety of the base and everyone in it. He had taken chances on not just his survival but that of every single man and woman in the city and everyone back on Earth… and all for the sake of his reluctance to lose a friend, his conviction that you didn't leave people behind. And he still believed that. And he knew in his heart that, given the choice, he'd do the same thing again. And he didn't know whether he should be proud of that… or terrified by it.

The next few hours in the isolation room had felt like an eternity.

Eventually Carson and his medical team had decided that, based on the timescale of Elizabeth's collapse following the attack by Niam, if John had been infected, there'd be signs of it by now and they'd cut him loose.

The first thing he did was go looking for Elizabeth. It was kinda dumb really… he knew she was okay, had been assured by Carson that she was fully recovered, 100 clear of nanites, but he needed to see for himself. He needed to talk to her, to see her awake and aware and alive… he needed a picture in his head to replace the last memory he had of talking with Elizabeth… the one that had ended with him cradling her unresponsive body in his arms and screaming for Carson.

He found her, of course, in the control room – ironically, right where she'd been when he'd last spoken to her, so many hours ago. The sense of relief at seeing her back on her feet was tempered by the unwelcome flood of memories… of the distant look in her eyes, of the control room shuddering around him, Elizabeth dropping suddenly to the floor, of the gate shutting down, leaving him alone in the doomed city… Memories, some of them real, some of them not; all of them vivid and disturbing.

He fixed a smile on his face and kept his tone light as he spoke, jolting Elizabeth from her reverie. She was shaken too, he could see it, and the pair of them stepped carefully around the conversation, shying away from the real depth of emotion lurking beneath. When she turned contemplative he cut her off, offering platitudes, and when she grew melancholy he tried to joke but it fell flat and he saw the real fear in her eyes as she told him, "John ... don't."

He felt like he wanted to say something, wanted to explain to her… to make her understand that he knew what he had risked, that he'd done it anyway, that'd he'd do it again in a heartbeat… and that that scared him. But the words stuck in his chest, just like they always did, and so he offered her the best he could give, an apology and a smile, and left her to her sombre thoughts.

When he finally went to bed, he dreamed of Atlantis exploding and dying. And in his dreams, he saw not the false memories of the Asuran mindprobe, not the ticking bomb that would end his life along with the city's in a last effort to protect Earth. Instead he saw the city fall by his own hand, by his negligence, because of his recklessness. And he saw it over and over again as he made the same choice over and over again; one risk too many, one bullet he couldn't dodge, one final, fatal choice that resulted in disaster.

He woke early and didn't bother trying to go back to sleep.

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**Fin.**


End file.
